Abstract: We analyzed the archaeal community in tropical aquaculture farm sediments in Dapeng Cove, located in the southwest of Daya Bay, southern China. Sediment cores samples (5 cm and 30 cm in depth) were collectedby a core-sampler in summer (August, 2014). Results show that the abundance of archaea in deep layers was higher than that in surface layer. The dominant species in surface and deep layers were Class Thermoplasma, Phylum Euryarchaeota, and Class MCG (Miscellaneous Crenarchaeotic Group), Phylum Crenarchaeota. In general, the abundance of Crenarchaeota was higher than that of Euryarchaeota. The abundance of predominant species was higher in aquaculture farms than in non-aquaculture area. The difference in archaeal community structure between surface and deep layers was more significant in aquaculture farms than that in non-aquaculture area. Results indicate that the archaeal community structure might be affected byintensive aquaculture activities, whose underlying mechanism needs further study.